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THE REGULATION OF GENE EXPRESSION IN GRAPEVINE FLOWERING PROCESS
Get PDFThe climate changes are rapidly mutating the delicate balances which established among different living organisms in relation to environments and ecosystems. These balances are the result of a millennial adaptation process flowing slowly and inexorably up to continuatively reach an ever new and dynamic equilibrium, which reward the suitable organisms and mow the unadapt ones. Global warming, ecosystems destruction and catastrophic extreme events are increasingly rising from uncontrolled anthropic activities and the area par excellence that is suffering the heaviest repercussions is agriculture. It is of primary importance that the next goal for humankind be identified in implementation of productive systems featured by low inputs, maximization of process efficiency and high resilience to the wide fluctuations of biological and environmental parameters featuring the present era. In this regard, biotechnology could dress a first-rate role by unrevealing the plant fully potential hidden in the molecular mechanisms at the basis of crop growth, development and production. It is precisely at this point that this work fits in, or rather to try to clarify the genetic relationships at the basis of flowering process in grapevine (Vitis vinifera L.). Even if grapevine is a crop typically characterized by a dominance of vegetative propagation, there are several reasons why to be interest in shading light on this particular issue. In contrast to the historical and cultural legacies that see viticulture as an extremely conservative discipline, the importance of conventional genetic improvement of varieties is increasingly affirming. The reason for this is soon individuated if we think at plant cross as very powerful item to generate new genetic variability to employ for breeding programmes aimed to the constitutions of grapevine varieties featured by pathogen resistance, abiotic stress tolerance and specific qualitative traits of the production. By the way, quantitative and qualitative traits of the production are directly influenced by flowering, which represents the first constituted step of the reproductive phase leading to the development of the main product, the berry. The structure of the flower and the architecture of the inflorescence affect the organization of the bunch, with many consequences at the production level. Knowing all the genetic relationships and the molecular mechanisms behind the anthesis in every single actor role means to be able to control the entire process and to address the production in a targeted manner. To improve this kind of knowledge, it was decided to dissect grapevine flower in each single whorl: calyx, calyptra, filament, anther, stigma, ovary, and embryo in two time points representing pre- and post-anthesis phases. To identify hub genes that unequivocally distinguish the different tissues providing insights into the molecular mechanisms that are at the basis of floral whorls and tissue development, it was used an RNA-Seq approach, producing a grapevine flower transcriptome atlas. Several analytical techniques were used to gradually narrow the field, in particular weighted gene coexpression network analysis (WGCNA) and tau analysis were applied to isolate clusters of genes showing a similar expression pattern and high or absolute specificity for a given tissue, respectively. Several transcription factors (TFs) were identified within the various whorls and a subset of 17 of them was selected to be analysed with a novel technique, the DAP-Seq. This assay allows the identification of the binding sites within a genome for a given TF through the hybridization of the in vitro expressed TF-protein with the fragments of gDNA. Taking advantage from the adaptation of DAP-Seq to grapevine, the entire cistrome of the 17 TFs was discovered and the targets were crossed with the WGCNA and tau analysis data in order to have back for each TF a list of directly regulated targets, characterized by a similar [...]The climate changes are rapidly mutating the delicate balances which established among different living organisms in relation to environments and ecosystems. These balances are the result of a millennial adaptation process flowing slowly and inexorably up to continuatively reach an ever new and dynamic equilibrium, which reward the suitable organisms and mow the unadapt ones. Global warming, ecosystems destruction and catastrophic extreme events are increasingly rising from uncontrolled anthropic activities and the area par excellence that is suffering the heaviest repercussions is agriculture. It is of primary importance that the next goal for humankind be identified in implementation of productive systems featured by low inputs, maximization of process efficiency and high resilience to the wide fluctuations of biological and environmental parameters featuring the present era. In this regard, biotechnology could dress a first-rate role by unrevealing the plant fully potential hidden in the molecular mechanisms at the basis of crop growth, development and production. It is precisely at this point that this work fits in, or rather to try to clarify the genetic relationships at the basis of flowering process in grapevine (Vitis vinifera L.). Even if grapevine is a crop typically characterized by a dominance of vegetative propagation, there are several reasons why to be interest in shading light on this particular issue. In contrast to the historical and cultural legacies that see viticulture as an extremely conservative discipline, the importance of conventional genetic improvement of varieties is increasingly affirming. The reason for this is soon individuated if we think at plant cross as very powerful item to generate new genetic variability to employ for breeding programmes aimed to the constitutions of grapevine varieties featured by pathogen resistance, abiotic stress tolerance and specific qualitative traits of the production. By the way, quantitative and qualitative traits of the production are directly influenced by flowering, which represents the first constituted step of the reproductive phase leading to the development of the main product, the berry. The structure of the flower and the architecture of the inflorescence affect the organization of the bunch, with many consequences at the production level. Knowing all the genetic relationships and the molecular mechanisms behind the anthesis in every single actor role means to be able to control the entire process and to address the production in a targeted manner. To improve this kind of knowledge, it was decided to dissect grapevine flower in each single whorl: calyx, calyptra, filament, anther, stigma, ovary, and embryo in two time points representing pre- and post-anthesis phases. To identify hub genes that unequivocally distinguish the different tissues providing insights into the molecular mechanisms that are at the basis of floral whorls and tissue development, it was used an RNA-Seq approach, producing a grapevine flower transcriptome atlas. Several analytical techniques were used to gradually narrow the field, in particular weighted gene coexpression network analysis (WGCNA) and tau analysis were applied to isolate clusters of genes showing a similar expression pattern and high or absolute specificity for a given tissue, respectively. Several transcription factors (TFs) were identified within the various whorls and a subset of 17 of them was selected to be analysed with a novel technique, the DAP-Seq. This assay allows the identification of the binding sites within a genome for a given TF through the hybridization of the in vitro expressed TF-protein with the fragments of gDNA. Taking advantage from the adaptation of DAP-Seq to grapevine, the entire cistrome of the 17 TFs was discovered and the targets were crossed with the WGCNA and tau analysis data in order to have back for each TF a list of directly regulated targets, characterized by a similar [...
The Mitochondrial Genome Assembly of Fennel (Foeniculum vulgare) Reveals Two Different atp6 Gene Sequences in Cytoplasmic Male Sterile Accessions
No full textCytoplasmic male sterility (CMS) has always aroused interest among researchers and breeders, being a valuable resource widely exploited not only to breed F1 hybrid varieties but also to investigate genes that control stamen and pollen development. With the aim of identifying candidate genes for CMS in fennel, we adopted an effective strategy relying on the comparison between mitochondrial genomes (mtDNA) of both fertile and sterile genotypes. mtDNA raw reads derived from a CMS genotype were assembled in a single molecule (296,483 bp), while a draft mtDNA assembly (166,124 nucleotides, 94 contigs) was performed using male fertile sample (MF) sequences. From their annotation and alignment, two atp6-like sequences were identified. atp6-, the putative mutant copy with a 300 bp truncation at the 5'-end, was found only in the mtDNA of CMS samples, while the wild type copy (atp6 +) was detected only in the MF mtDNA. Further analyses (i.e., reads mapping and Sanger sequencing), revealed an atp6 + copy also in CMS samples, probably in the nuclear DNA. However, qPCRs performed on different tissues proved that, despite its availability, atp6 + is expressed only in MF samples, while apt6-mRNA was always detected in CMS individuals. In the light of these findings, the energy deficiency model could explain the pollen deficiency observed in male sterile flower. atp6-could represent a gene whose mRNA is translated into a not-fully functional protein leading to suboptimal ATP production that guarantees essential cellular processes but not a high energy demand process such as pollen development. Our study provides novel insights into the fennel mtDNA genome and its atp6 genes, and paves the way for further studies aimed at understanding their functional roles in the determination of male sterility
Genomics of flower identity in grapevine (Vitis vinifera L.)
Get PDFThe identity of the four characteristic whorls of typical eudicots, namely, sepals, petals, stamens, and carpels, is specified by the overlapping action of homeotic genes, whose single and combined contributions have been described in detail in the so-called ABCDE model. Continuous species-specific refinements and translations resulted in this model providing the basis for understanding the genetic and molecular mechanisms of flower development in model organisms, such as Arabidopsis thaliana and other main plant species. Although grapevine (Vitis vinifera L.) represents an extremely important cultivated fruit crop globally, studies related to the genetic determinism of flower development are still rare, probably because of the limited interest in sexual reproduction in a plant that is predominantly propagated asexually. Nonetheless, several studies have identified and functionally characterized some ABCDE orthologs in grapevine. The present study is intended to provide a comprehensive screenshot of the transcriptional behavior of 18 representative grapevine ABCDE genes encoding MADS-box transcription factors in a developmental kinetic process, from preanthesis to the postfertilization stage and in different flower organs, namely, the calyx, calyptra, anthers, filaments, ovary, and embryos. The transcript levels found were compared with the proposed model for Arabidopsis to evaluate their biological consistency. With a few exceptions, the results confirmed the expression pattern expected based on the Arabidopsis data
Past, present and future of genetic strategies to control tolerance to the main fungal and oomycete pathogens in grapevine
No full textThe production of high-quality wines is strictly related to the correct management of the vineyard, which guarantees good yields and grapes with the right characteristics required for subsequent vinification. Winegrowers face a variety of challenges during the grapevine cultivation cycle: the most notorious are fungal and oomycete diseases such as downy mildew, powdery mildew, and gray mold. If not properly addressed, these diseases can irremediably compromise the harvest, with disastrous consequences for the production and wine economy. Conventional defense methods used in the past involved the use of chemical pesticides. However, such approaches are in conflict with the growing attention on environmental sustainability and shifts from the uncontrolled use of chemicals to the use of integrated approaches for crop protection. Improvements in genetic knowledge and the availability of novel biotechnologies have created new scenarios for possibly producing grapes with a reduced, if not almost zero, impact. Here, the main approaches used to protect grapevines from fungal and oomycete diseases are reviewed, starting from conventional breeding, which allowed the establishment of new resistant varieties, followed by biotechnological methods, such as transgenesis, cisgenesis, intragenesis and genome editing, and ending with more recent perspectives concerning the application of new products based on RNA interference (RNAi) technology. Evidence of their effectiveness, as well as potential risks and limitations based on the current legislative situation, are critically discussed
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Boosting grapevine breeding for climate-smart viticulture: from genetic resources to predictive genomics
Get PDFThe multifaceted nature of climate change is increasing the urgency to select resilient grapevine varieties, or generate new, fitter cultivars, to withstand a multitude of new challenging conditions. The attainment of this goal is hindered by the limiting pace of traditional breeding approaches, which require decades to result in new selections. On the other hand, marker-assisted breeding has proved useful when it comes to traits governed by one or few genes with great effects on the phenotype, but its efficacy is still restricted for complex traits controlled by many loci. On these premises, innovative strategies are emerging which could help guide selection, taking advantage of the genetic diversity within the Vitis genus in its entirety. Multiple germplasm collections are also available as a source of genetic material for the introgression of alleles of interest via adapted and pioneering transformation protocols, which present themselves as promising tools for future applications on a notably recalcitrant species such as grapevine. Genome editing intersects both these strategies, not only by being an alternative to obtain focused changes in a relatively rapid way, but also by supporting a fine-tuning of new genotypes developed with other methods. A review on the state of the art concerning the available genetic resources and the possibilities of use of innovative techniques in aid of selection is presented here to support the production of climate-smart grapevine genotypes
Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family
Get PDFThis review highlights -omics research in Solanaceae family, with a particular focus on resilient traits. Extensive research has enriched our understanding of Solanaceae genomics and genetics, with historical varietal development mainly focusing on disease resistance and cultivar improvement but shifting the emphasis towards unveiling resilience mechanisms in genebank-preserved germplasm is nowadays crucial. Collecting such information, might help researchers and breeders developing new experimental design, providing an overview of the state of the art of the most advanced approaches for the identification of the genetic elements laying behind resilience. Building this starting point, we aim at providing a useful tool for tackling the global agricultural resilience goals in these crops
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